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Zinc in PDB 6ofd: The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase

Enzymatic activity of The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase

All present enzymatic activity of The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase:
3.1.3.2;

Protein crystallography data

The structure of The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase, PDB code: 6ofd was solved by D.Feder, G.Schenk, L.W.Guddat, W.M.Hussein, R.P.Mcgeary, M.W.Kan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.05 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.174, 126.174, 298.044, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 19.9

Other elements in 6ofd:

The structure of The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase (pdb code 6ofd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase, PDB code: 6ofd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6ofd

Go back to Zinc Binding Sites List in 6ofd
Zinc binding site 1 out of 4 in the The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:26.5
occ:1.00
 NE2 A:HIS286 2.0 22.8 1.0
ND1 A:HIS323 2.2 25.3 1.0
OD1 A:ASN201 2.2 27.9 1.0
O A:HOH619 2.2 34.0 1.0
OD2 A:ASP164 2.2 23.3 1.0
CE1 A:HIS286 2.9 19.7 1.0
CD2 A:HIS286 3.1 20.0 1.0
CE1 A:HIS323 3.1 25.1 1.0
CG A:ASP164 3.1 24.5 1.0
CG A:HIS323 3.2 24.2 1.0
OBG A:MF1517 3.2 38.0 0.5
CG A:ASN201 3.3 28.5 1.0
CA A:HIS323 3.3 19.1 1.0
FE A:FE502 3.4 27.2 0.8
OD1 A:ASP164 3.5 24.4 1.0
CB A:HIS323 3.5 16.8 1.0
OD2 A:ASP135 3.6 29.0 1.0
ND2 A:ASN201 3.9 32.1 1.0
O A:HIS323 4.1 25.6 1.0
ND1 A:HIS286 4.1 19.6 1.0
CG A:HIS286 4.2 21.3 1.0
C A:HIS323 4.2 23.7 1.0
N A:HIS323 4.2 23.4 1.0
N A:ASN201 4.2 20.7 1.0
NE2 A:HIS323 4.2 21.8 1.0
CD2 A:HIS323 4.3 22.4 1.0
PBE A:MF1517 4.4 44.2 0.5
CB A:ASP164 4.4 22.7 1.0
CB A:ASN201 4.4 25.0 1.0
CD2 A:HIS202 4.5 28.4 1.0
OBH A:MF1517 4.5 44.9 0.5
CG A:ASP135 4.8 24.2 1.0
OBF A:MF1517 4.8 46.0 0.5
CA A:ASN201 4.9 22.9 1.0
OH A:TYR253 4.9 24.3 1.0

Zinc binding site 2 out of 4 in 6ofd

Go back to Zinc Binding Sites List in 6ofd
Zinc binding site 2 out of 4 in the The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:27.6
occ:1.00
 NE2 B:HIS286 2.0 24.9 1.0
OD1 B:ASN201 2.1 28.1 1.0
ND1 B:HIS323 2.2 22.3 1.0
OD2 B:ASP164 2.3 27.9 1.0
O B:HOH847 2.5 35.5 1.0
CE1 B:HIS286 2.9 22.4 1.0
CD2 B:HIS286 3.1 22.0 1.0
CE1 B:HIS323 3.1 23.9 1.0
CG B:ASP164 3.1 26.4 1.0
CG B:HIS323 3.2 23.2 1.0
CA B:HIS323 3.3 25.3 1.0
FE B:FE502 3.3 28.5 0.7
CG B:ASN201 3.3 27.2 1.0
OD1 B:ASP164 3.3 23.6 1.0
CB B:HIS323 3.5 20.7 1.0
OD2 B:ASP135 3.7 25.3 1.0
ND2 B:ASN201 4.0 32.7 1.0
O B:HIS323 4.1 26.2 1.0
ND1 B:HIS286 4.1 23.9 1.0
CG B:HIS286 4.2 22.4 1.0
C B:HIS323 4.2 24.8 1.0
N B:HIS323 4.2 22.0 1.0
NE2 B:HIS323 4.2 22.7 1.0
CD2 B:HIS323 4.3 22.7 1.0
N B:ASN201 4.3 20.6 1.0
CD2 B:HIS202 4.3 24.3 1.0
CB B:ASN201 4.4 25.2 1.0
CB B:ASP164 4.5 21.9 1.0
CG B:ASP135 4.8 24.6 1.0
OH B:TYR253 4.8 23.6 1.0
CA B:ASN201 4.9 22.2 1.0

Zinc binding site 3 out of 4 in 6ofd

Go back to Zinc Binding Sites List in 6ofd
Zinc binding site 3 out of 4 in the The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:22.5
occ:0.92
 NE2 D:HIS286 2.0 21.4 1.0
ND1 D:HIS323 2.1 20.8 1.0
OD1 D:ASN201 2.2 27.6 1.0
OD2 D:ASP164 2.3 25.1 1.0
O D:HOH784 2.3 30.4 1.0
CE1 D:HIS286 3.0 19.2 1.0
CE1 D:HIS323 3.0 25.1 1.0
CD2 D:HIS286 3.1 19.0 1.0
CG D:HIS323 3.1 22.5 1.0
CG D:ASP164 3.2 24.8 1.0
CG D:ASN201 3.3 29.9 1.0
CA D:HIS323 3.3 19.8 1.0
FE D:FE502 3.4 28.2 0.6
OD1 D:ASP164 3.5 24.2 1.0
CB D:HIS323 3.5 21.1 1.0
OD2 D:ASP135 3.6 26.8 1.0
ND2 D:ASN201 3.9 27.1 1.0
O D:HIS323 4.1 22.1 1.0
ND1 D:HIS286 4.1 21.4 1.0
NE2 D:HIS323 4.1 19.8 1.0
CG D:HIS286 4.2 22.3 1.0
C D:HIS323 4.2 24.6 1.0
CD2 D:HIS323 4.2 21.9 1.0
N D:HIS323 4.2 20.4 1.0
N D:ASN201 4.3 22.6 1.0
CD2 D:HIS202 4.3 28.2 1.0
CB D:ASN201 4.4 23.8 1.0
CB D:ASP164 4.5 20.6 1.0
CG D:ASP135 4.8 26.6 1.0
OH D:TYR253 4.8 22.0 1.0
CA D:ASN201 4.9 22.8 1.0
NE2 D:HIS202 4.9 27.8 1.0

Zinc binding site 4 out of 4 in 6ofd

Go back to Zinc Binding Sites List in 6ofd
Zinc binding site 4 out of 4 in the The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:26.5
occ:1.00
 NE2 C:HIS286 2.0 21.9 1.0
OD1 C:ASN201 2.0 28.4 1.0
ND1 C:HIS323 2.1 20.6 1.0
OD2 C:ASP164 2.3 23.7 1.0
O C:HOH623 2.4 32.9 1.0
CE1 C:HIS286 2.9 22.3 1.0
CE1 C:HIS323 3.0 24.1 1.0
CD2 C:HIS286 3.1 17.5 1.0
CG C:ASP164 3.1 26.0 1.0
CG C:HIS323 3.2 21.7 1.0
CG C:ASN201 3.2 27.6 1.0
CA C:HIS323 3.4 21.4 1.0
OD1 C:ASP164 3.5 21.5 1.0
FE C:FE502 3.5 25.3 0.6
CB C:HIS323 3.6 19.3 1.0
OD2 C:ASP135 3.7 29.5 1.0
ND2 C:ASN201 3.9 27.2 1.0
ND1 C:HIS286 4.1 20.0 1.0
O C:HIS323 4.1 23.7 1.0
NE2 C:HIS323 4.1 21.9 1.0
N C:ASN201 4.2 23.1 1.0
CG C:HIS286 4.2 24.0 1.0
C C:HIS323 4.2 24.7 1.0
CD2 C:HIS323 4.3 21.6 1.0
N C:HIS323 4.3 23.9 1.0
CB C:ASN201 4.3 26.1 1.0
CB C:ASP164 4.4 18.0 1.0
CD2 C:HIS202 4.5 26.4 1.0
OH C:TYR253 4.7 22.3 1.0
CA C:ASN201 4.8 22.6 1.0
CG C:ASP135 4.8 25.5 1.0
N C:HIS202 5.0 21.1 1.0

Reference:

D.Feder, M.W.Kan, W.M.Hussein, L.W.Guddat, G.Schenk, R.P.Mcgeary. Synthesis, Evaluation and Structural Investigations of Potent Purple Acid Phosphatase Inhibitors As Drug Leads For Osteoporosis. Eur.J.Med.Chem. V. 182 11611 2019.
ISSN: ISSN 0223-5234
PubMed: 31445230
DOI: 10.1016/J.EJMECH.2019.111611
Page generated: Tue Oct 29 04:20:37 2024

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